Commit cbd10c09 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

linter: allow setting output format with actions

parent 76bf9bfc

lib/galaxy/tool_util/linters/outputs.py

+2 −0
Original line number Diff line number Diff line
@@ -63,6 +63,8 @@ def __check_format(node, lint_ctx, allow_ext=False): 
        lint_ctx.warn(f"Tool {node.tag} output '{node.attrib.get('name', 'with missing name')}' should use either format_source or format/ext", node=node)

    if "format_source" in node.attrib:

        return True

    if node.find(".//action[@type='format']") is not None:

        return True

    # if allowed (e.g. for discover_datasets), ext takes precedence over format

    fmt = None

    if allow_ext:

test/unit/tool_util/test_tool_linters.py

+28 −0
Original line number Diff line number Diff line
@@ -442,6 +442,25 @@ OUTPUTS_COLLECTION_FORMAT_SOURCE = """ 
</tool>

"""



# check that setting format with actions is supported

OUTPUTS_FORMAT_ACTION = """

<tool>

    <outputs>

        <data name="output">

            <actions>

                <conditional name="library.type">

                    <when value="paired">

                        <action type="format">

                            <option type="from_param" name="library.input_2" param_attribute="ext" />

                        </action>

                    </when>

                </conditional>

            </actions>

        </data>

    </outputs>

</tool>

"""



# check that linter does not complain about missing format if from_tool_provided_metadata is used

OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA = """

<tool>
@@ -1102,6 +1121,15 @@ def test_outputs_collection_format_source(lint_ctx): 
    assert not lint_ctx.error_messages





def test_outputs_format_action(lint_ctx):

    tool_source = get_xml_tool_source(OUTPUTS_FORMAT_ACTION)

    run_lint(lint_ctx, outputs.lint_output, tool_source)

    assert len(lint_ctx.info_messages) == 1

    assert not lint_ctx.valid_messages

    assert not lint_ctx.warn_messages

    assert not lint_ctx.error_messages





def test_outputs_discover_tool_provided_metadata(lint_ctx):

    tool_source = get_xml_tool_source(OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA)

    run_lint(lint_ctx, outputs.lint_output, tool_source)